The modified nucleotide queuosine (Q) is almost universally found in the anticodon wobble position of specific tRNAs. In many bacteria, biosynthesis of Q is modulated by a class of regulatory mRNA elements called riboswitches. The preQ1 riboswitch, found in the 5′UTR of bacterial genes involved in synthesis of the Q precursors preQ0 and preQ1, contains the smallest known aptamer domain. We report the solution structure of the preQ1 riboswitch aptamer domain from Bacillus subtilis bound to preQ1, which is a unique compact pseudoknot with three loops and two stems that encapsulates preQ1 at the junction between the two stems. The pseudoknot only forms in the presence of preQ1, and the 3′ A-rich tail of the aptamer domain is an integral part of the pseudoknot. In the absence of preQ1, the A-rich tail forms part of the antiterminator. These structural studies provide insight into riboswitch transcriptional control of preQ1 biosynthesis. © 2009 Elsevier Inc. All rights reserved.
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